A second base pair interaction between U3 small nucleolar RNA and the 5′-ETS region is required for early cleavage of the yeast pre-ribosomal RNA

Abstract

In eukaryotes, U3 snoRNA is essential for pre-rRNA maturation. Its 5′-domain was found to form base pair interactions with the 18S and 5′-ETS parts of the pre-rRNA. In Xenopus laevis, two segments of U3 snoRNA form base-pair interactions with the 5′-ETS region and only one of them is essential to the maturation process. In Saccharomyces cerevisiae, two similar U3 snoRNA–5′ ETS interactions are possible; but, the functional importance of only one of them had been tested. Surprisingly, this interaction, which corresponds to the non-essential one in X. laevis, is essential for cell growth and pre-rRNA maturation in yeast. In parallel with [Dutca et al. (2011) The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39, 5164–5180], here we show, that the second possible 11-bp long interaction between the 5′ domain of S. cerevisiae U3 snoRNA and the pre-rRNA 5′-ETS region (helix VI) is also essential for pre-rRNA processing and cell growth. Compensatory mutations in one-half of helix VI fully restored cell growth. Only a partial restoration of growth was obtained upon extension of compensatory mutations to the entire helix VI, suggesting sequence requirement for binding of specific proteins. Accordingly, we got strong evidences for a role of segment VI in the association of proteins Mpp10, Imp4 and Imp3.

Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis

“…As one of the core components in the small subunit processome, U3 snoRNP has been shown to have a conserved function in 18S rRNA biogenesis (8,17,23). Depletion of U3 snoRNA in yeast has been shown to lead to underaccumulation of mature 18S rRNA (37).…”

“…The U3 C/D box snoRNP shown to be universally conserved across eukaryotes is the core component of the small subunit processome essential for 18S rRNA processing (16,17). In plants, it has been reported that the U3 snoRNP forms a stable complex with nucleolin protein 1 (NUC1), which binds nascent pre-RNA at the 5′ ETS and specifically cleaves pre-rRNA at the P site (18)(19)(20).…”

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

“…The separating cleavage at A 2 as well as the other detectable cleavages in the pre-18S rRNA at sites A 0 and A 1 are dependent on the presence of the U3 snoRNA (originally referred to as snR17 in yeast) (Hughes and Ares 1991). While the U3 snoRNA belongs to the class of box C/D snoRNPs, it does not carry out rRNA methylation, but instead uses three short stretches of its 59 70 nt to base pair with three different sites in the 59ETS to effect prerRNA cleavage Tollervey 1992, 1995;Beltrame et al 1994;Hughes 1996;Mereau et al 1997;Sharma and Tollervey 1999;Borovjagin and Gerbi 2005;Dutca et al 2011;Marmier-Gourrier et al 2011). In general, the presence of the U3 snoRNA has been shown to be required for correct folding of the pre-rRNA (Dutca et al 2011).…”

Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast

“…The 5 ′ ETS is a noncoding region preceding the 18S and contains two essential binding sites, termed A and B here, for U3 snoRNA (Beltrame and Tollervey 1995;Dutca et al 2011;Marmier-Gourrier et al 2011). U3 also binds at two additional sites, called C and D here, in the 5 ′ end and the central region of 18S.…”